NAOMInova

Overview

NAOMInova enables the geometrical and chemical analysis of atoms surrounding a user-defined structure of interest. Substructures can be searched based on a user-defined set of protein structures. Users can also visualize the distribution of partner points. Two visualization options are available: the "set" visualization, i.e., the partner points surrounding the substructure, and the "pocket" visualization, i.e., the transformation of all partner points surrounding the substructure into a suitable binding site of interest. Diverse geometric - distance, angles, resolution - and chemical - atom type, location, amino acid - properties are available for more detailed analysis by filtering the results. The original complex is stored for each partner point, enabling an easy evaluation to find whether this point is of interest.

Software Availability

NAOMInova is freely available for non-commercial and academic users for Linux, MacOS, and Windows as part of our NAOMI ChemBio Suite. To download NAOMInova, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run NAOMInova. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Inhester, T.; Nittinger, E.; Sommer, K.; Schmidt, P.; Bietz, S.; Rarey, M. NAOMInova: Interactive Geometric Analysis of Noncovalent Interactions in Macromolecular Structures. J Chem Inf Model 2017, 57 (9), 2132-2142. DOI: https://doi.org/10.1021/acs.jcim.7b00291
Nittinger, E.; Inhester, T.; Bietz, S.; Meyder, A.; Schomburg, K. T.; Lange, G.; Klein, R.; Rarey, M. Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein-Ligand Interfaces. J Med Chem 2017, 60 (10), 4245-4257. DOI: https://doi.org/10.1021/acs.jmedchem.7b00101